I just finished assembling my prusa mendel and got all of the electronics wired up, and finally got pronterface to start moving some things around. I've gotten all 3 axises to find the home switch and stop, but for some reason the y motor keeps going in the same direction. I've swapped the motor and driver and neither seem to be the problem, I'm running out of ideas here. also the extruder temp is low even though the settings for it are correct, and I'm not sure where to adjust it.

I don't understand. You say all three axes find home and stop, but then you say the y axis keeps going. Does it stop or keep going? I think we needa better description of the problem.

Have you checked the end stop status. You can query it through pronterface wth the M119 gcode command.

when you press the + or - buttons for movement, it only goes in one direction, even after stopping correctly at the endstop, it rams into it further if i press one of the direction buttons. thankfully i had the stop held on with a twist tie so it didn't do much damage. I ended up changing the pins for the y axis over to the second extruder spot, which fixed it. there must be something wrong with the arduino or the board for that output. I still can't figure out why the hot end isn't getting hot enough, there must be something weird going on with the thermistor. it says it is at 180 but it is really around 60

sagi: Sounds like you have the wrong thermistor table configured.

after a few too many hours messing around with it and checking it with an ohmmeter I think the problem was my IR thermometer just wouldn't read it correctly. it seemed the thermistor was correct though.